


on the root, we stand tall

by FantasyDeath



Category: Naruto
Genre: Alternate Universe - Canon Divergence, Dubious Morality, Implied Human Experimentation, M/M, Minor Character Death, Moral Ambiguity, Original Character(s), Out of Character
Language: English
Status: Completed
Published: 2017-11-27
Updated: 2017-11-27
Packaged: 2019-02-05 23:53:45
Rating: Not Rated
Warnings: Creator Chose Not To Use Archive Warnings
Chapters: 1
Words: 3,863
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/12805131
Author URL: https://archiveofourown.org/users/FantasyDeath/pseuds/FantasyDeath
Summary: When Orochimaru is approached by Danzo to join his secret group, he has expectations. He expects to be allowed to do whatever experiments he wants, he expects, if not willing, then not missed test subjects, and he expects that when it all gets out, he'll take as many people down with him as he can. He very distinctly does not expect to accidentally take over Root. Really, it's not even a contingency plan.





	on the root, we stand tall

It began kind of like this:

Takahashi Yu was five years old when his parents died. Soon after, he was left at Konoha's orphanage, just one of dozens of children whose parents had been lost to war. His parents had both been tokubetsu jounin, good enough at their chosen specialties to be sent to the frontline, but not good enough to survive. They were both from civilian families and Yu had no-one once they were gone. At five years old, it seemed like the end of the world. 

Once he was six, he started at the shinobi academy together with almost all of the other orphans his age. He didn't excel and he didn't particularly stand out, being painfully average in almost everything. Everything but genjutsu, that is.

It seemed that he'd inherited his mother's talent with it. 

He was nine when he graduated from the academy just slightly above average, never able to succeed enough to truly stand out.

He was never given a team.

By the time he was ten, Takahashi Yu had ceased to exist. Instead there was 104, a shinobi working for Root who had already started taking assassination missions.

 

(Except it didn't start like that.)

 

No, maybe it was more like this:

At eight years old, Shun was already a veteran of Root. It was where he grew up, everything he knew. He could make his way through the base blindfolded (had done so before actually) and knew every single rule that was to be followed like the back of his hand. Lately though, lately, he'd found himself starting to doubt them. He'd gotten a roommate. 

Jun was two years younger then him, a girl and had just completed her training. 

She was bright-eyed and had a sense of innocence about her that confused him. She listened to every word he said like he was her superior and followed behind his every step. She liked flowers because they reminded her of her mother—who was sick in the hospital and Shun found himself wondering what exactly a mother did—and she had two younger brothers who both idolized her as well as a father that was a retired jounin. She'd joined Root because Danzo-sama promised he would pay for her mother's treatment. 

She died exactly three years, two months and five days after she became his roommate on her ninth mission when she protected her teammate instead of retreating.

Suddenly, their (his) room was terribly empty. Suddenly, he couldn't look at Danzo-sama when he gave his reports anymore. Suddenly, he found himself carefully observing the shinobi whose life she'd saved, for the first time in years feeling anger when it didn't seem to have mattered to them. Suddenly, he got a weird feeling in his chest whenever he saw the new recruits. Suddenly, things were _different._

Shun met Orochimaru of the Sannin for the first time at age thirteen.

 

(No, no, this isn't it either. Rewind a bit more and perhaps... yes, something like this.)

 

Kira was a civilian before she was recruited for Root.

She grew up in the red lights district, her mother dead by the time she was four from disease and her father unknown. She had no siblings or close friends, no-one that would miss her should she suddenly go missing and was young enough that she could still be shaped into something useful, even if she was to old to be accepted at the academy for ninjas. All of this made her ideal and she was twelve when she moved into the base below the Hokage mountain. 

She didn't leave it for eighteen months.

When she finally did, it was without a name, just a number, a katana in her hand and a mission that she _could not fail._  

She failed.

Failed, failed, failed.

(It was such an ugly word, how had she never realized that before?)

She returned to the base without the scroll she had been sent to retrieve, bloodied and sore and filled with a fear she had been taught not to acknowledge. There was a limp when she walked, a hitch in her breath that pointed towards broken ribs and somewhere along the way, she'd lost her katana. 

She reported her failure to Danzo-sama, of course she did, and it was the first time she didn't resent him, when he told her that he still had a use for her.

Four days later, healed but for the bruises, she reported to her new superior in a smaller base and watched with a detached sort of curiosity as Orochimaru—of the Sannin and even she had heard of him and his legendary team—cut someone open on a metal table, pulled them apart and put them back together again.

She was fifteen when she once again became Kira.

 

(Hmm... better, but not good enough. How about this?)

 

Matsumoto Naoki was painfully shy, even at eleven. 

He never looked anyone in the eyes, was never within touching distance and his looks were generic, brown hair, tanned skin and grey eyes. His genin team didn't know what to make of him and their teacher didn't have the time to solve anything personal as they were scouts. Both his parents were still alive and in good health.

Naoki was of no special interest to anyone, much less Shimura Danzo.

Then he returned three weeks late from a standard mission that had devolved into a good old-fashioned ambush by Iwa, dragging the dead body of his jounin sensei behind him.

Interrogation by T&I revealed that he had a passive Bloodline Limit, one that kept anything that effected the mind from working on him. The team of Iwa shinobi that had killed his team had used ninjutsu to make them fight amongst themselves and in the end, their sensei had killed himself to keep from hurting his students. It hadn't helped, Naoki's teammates were still dead and their bodies in possession of Iwa.

Within a month, his parents were dead and he had been relocated to Root's base. All knowledge of his Bloodline Limit had been erased and Naoki had been left with Orochimaru for the purpose of figuring out if his Kekkei Genkai could be transferred to fellow Konoha Shinobi.

 

(Closer, closer, closer. Now turn it this way.)

 

There was a lump in his throat every time he tried to swallow. 

Hotaru—formerly Yuki, formerly Nai, formerly Mikoto—was five months into his infiltration mission of Yugakure when he was recalled. There hadn't been anything of interest to report, Yugakure was still in the process of turning into a tourist spot, still trying to leave the ninja stuff behind them to the disgust of its shinobi. The only logical reason for him to be recalled was a new mission or his disposal. He didn't think he'd outlived his usefulness, but then again, he couldn't follow the way Danzo-sama thought. At twenty years old, he knew that knowing to much of Root was dangerous business because it meant you became a liability and he'd worked hard to never interact with his comrades enough to know anything sensitive. 

Still, there was the lingering thought that he'd done something wrong, heard something he wasn't supposed to and now he would be gotten rid of.

Nonetheless, he made his way to the facility marked on the map he'd been given, determined to follow whatever order he got.

Once there, he was let in by a Root member and shown to a large open room in which there were many many containers with people in a faintly glowing green liquid just floating inside, all of them different ages, but most of them younger then him. Not a sound escaped him as he memorized everything he saw, certain that this would be part of his mission. He didn't try to deny what he saw, didn't feel any need to free them, didn't start planning to spill this secret to the Hokage.

It was a mission and it didn't matter how immoral a normal shinobi of Konoha would call it.

Hotaru was a part of Root, had been for over a decade. He'd done his fair share of assassination missions though his specialty was infiltration and sabotage if the situation demanded it. He lost whatever shred of morality he still had when he killed his only friend in Root on Danzo-sama's order.

After several long minutes of waiting, the door he had entered through was opened once again, this time letting in a girl younger than him but with the hardness to her that everyone in Root, regardless of age, shared. She took in everything about him, from his long black hair to his nondescript kimono and blue eyes. Her gaze laid on his chest for just a second, clearly wondering on his gender, but like any Root shinobi, not considering it anything of importance. His last two missions had both been spent playing a girl and perhaps he'd gotten just a little too into character, as he hadn't left his nice (but still practical, the was important) clothes behind for his uniform like he should have.

The girl didn't waste any time.

"You have been relocated to Orochimaru-sama's command. Your new mission is to travel the Elemental Countries in search of young people with potential, no-one over the age of seventeen. Once found, you are to either kidnap them and bring them here forcefully, or convince them to come on their own violation. Preferably those with Bloodline Limits, but it is not a must. Make sure they have no-one too interested in them that could start asking questions. If they are a shinobi or not, as well as age, gender and nationality are of no importance. Do you understand?"

"Understood." Hotaru stated emotionlessly.

 

(Yes, yes, yes, just a little more.)

 

Itou Reiko was one week into her training as a member of Root when she was transferred from the Base to a facility at the outskirts of Konohagakure no Sato.

At twelve years old, she was a late graduate of the shinobi academy from a minor shinobi clan. Her clan, as small as they were, had survived the various wars on their specific style of Kenjutsu and she was no different. She was excellent at her clan techniques, having practiced them since she had learned how to walk, but average at everything else. Root was a chance to make her family proud. 

Her last chance.

The facility she was transferred to was smaller than the base, but still far bigger then she would expect under a village. It was made up of winding hallways and large open rooms. The shinobi that showed her the way (Shun, the only ninja of Root that hadn't looked at her funny when she asked for their name) pointed out the different locations and made it clear that she was to practice with the shinobi in the base until she was at an acceptable level, at which point she'd be assigned to guard duty together with him.

She was to report directly to Orochimaru—and only Orochimaru—and keep everything she witnessed or heard strictly secret. Failure to do so would result in her being transferred out and relocated for additional training. And after the hell her first week had been, that wasn't something she looked forward to. 

Finally, she was shown to the study in which Orochimaru-sama was.

Orochimaru wasn't like she'd pictured him. After all the stories her parents and peers had told her, she'd expected greasy hair, pale yellowing skin and creepy demonic eyes. What she saw was a woman or man wearing a grey yukata, with graceful black hair twisted into a bun at the back of the head, beautiful golden eyes and pretty pale skin. There was nothing monstrous about him and she wondered how her comrades could have gotten it so wrong.

 

(Now go back to the beginning and try again.)

 

Orochimaru was twenty-six, almost thirty, when he was finally entirely alone in his village. His team was gone, scattered to the wind and his sensei could barely bear to look at him anymore. The villagers, both shinobi and civilians alike, avoided him and hurried out of his way.

There was a hole in his chest where his heart should be.

Danzo pushed all of the right buttons.

Within a week, he was presented with a facility he controlled, with state of the art labs and the best equipment available. Test subjects followed within another.

Subordinates followed after.

Orochimaru was used to being feared and despised for his actions and lack of reactions. He was used to being looked on as something unknown, something _dangerous_. He was used to being discarded as human, underestimated because he looked beautiful rather than handsome. He was used to being pushed aside, left behind and forgotten. It was bewildering, the way these subordinates _didn't_.

They didn't give him any looks of contempt, of suspicion. There were no whispering words behind his back, no blunt words of dislike and distrust to his face. No withering looks or refusal to obey orders simply because he was the one giving them.

It was the first time in his life that anyone had ever _respected_ him.

Even when the experiments failed, some in truly gruesome ways, they never turned away from him. They did their duty, handed him the tools he asked for, disposed of the bodies as he instructed, and never once did their facial expressions betray them. There was no disgust in their eyes as they looked at him work, no sympathy for the test subjects, no reactions at all. They did their jobs and they did them well.

Orochimaru was stunned by it.

He found himself remembering their names and what they looked like. He helped them train once in a while, when he had nothing else to do. Even Naoki, shy sweet Naoki, was treated with a gentleness he had never afforded his experiments before. It wasn't so much that he had changed, because he was just as cruel as he always had been on the battlefield, just as merciless, just as hard to understand by _normal_ people. But the members of Root could never be classified as normal. They were just as broken, just as _wrong_ , as he was. It made him connect with them in a way he never had with anyone before.

He was selfish and cruel and no-one in their right mind would ever accept him for who he was. Making connections (tentative ones) with like-minded people was something everyone strove to do, and something he had never been able to. He was possessive of what he considered his and that was what his subordinates were. _His_. His to mold, his to train, his to kill. 

Orochimaru found himself gradually starting to relax as Hotaru dropped off both recruits and budding test subjects, he got used to the way Kira was always following him around, keeping careful note of everything he did. Yu, constantly hiding in shadows and darkness, only ever emerging when one of the subjects managed to get loose and killing them. 

Life wasn't perfect—Sensei still couldn't look at him and his suspicion mounted every day—but it was as good as it was ever going to get. From time to time, a Root member was transferred in or out and Orochimaru sometimes visited the main base, because when this was all discovered (they lived in a shinobi village, _of course_ it was going to be discovered) Orochimaru was going to bring as many people down with him as possibly he could. 

It probably wasn't a good life or even a halfway-decent one, but it was all Orochimaru was ever going to get. He just didn't expect that Root members had a tendency to get... _attached_. 

 

(Good, good, but that's not all. Try and see the bigger picture.)

 

Root was a collection of emotionally traumatized people who were conditioned to be loyal to Danzo over the village. The missions they ran both helped and ruined things for Konoha, every action they took bringing them closer to war. They were loyal, they were killers and they were shadows. The only purpose they had was Danzo-sama's orders. 

But Danzo didn't practice what he preached.

They were to be emotionless soldiers that could only kill, but Danzo never once attempted to rid himself of his own emotions. They were to be perfect beings that prioritized the village and mission above all else, but Danzo disregarded the Hokage's words as that of a fool's and never listened. Moreover, Danzo didn't pay them much attention once they'd finished their training. He picked favorites and killed off those that he deemed threats, but otherwise he barely even looked at them.

He was arrogant and a warmonger and maybe he was a good shinobi, but he wasn't very good at loyalty. Much less loyalty to the army he had built and then proceeded to discard.

Root members were taught to stand in the shadows and observe, never to let anyone know they were there. Naturally, they knew the value of information. Orochimaru was an unknown variable, one that would be the superior of some and the target of others. It was only natural for them to learn everything about him.

In the process, they discovered something more.

It wasn't that they were suddenly less loyal to Danzo-sama or that they doubted their cause. It wasn't that they had thoughts of spilling secrets to the village proper. It was that Orochimaru was a good teacher and he was less than normal and made no excuses. He knew he was dangerous and didn't bother to pretend he wasn't like Danzo-sama. When a few of them gathered up the resolve to ask him questions, they got honest answer and when he helped them train, they always improved. In the end, he was everything Danzo-sama had wanted them to be, emotionless and willing to do whatever was necessary for Konoha.

So they observed him, watched him, noted down how he acted and studied his every move. They found flaws and perfections and things that didn't make any sense, like they way he was treated by the villagers—and shinobi—he protected. The shift wasn't instantaneous nor fast and it didn't really change things. It was just that Orochimaru was like them in a way Danzo-sama wasn't and that... changed things. 

Root members were to stay in the shadows. They were conditioned to be loyal to Danzo before the village, but Danzo never returned the favor. But Orochimaru was loyal and a genius with a brilliant mind that had nothing against helping them train. Orochimaru listened to what they said and had nothing against it when they claimed names of their own.

In the end, something had to break.

 

(Ah, we're almost there.)

 

It began kind of like this:

Orochimaru was an outcast in his own village, one he had sworn to protect in an era fraught with wars and dangers. He was lured (not really) by Danzo to become a member of Root, where he would be allowed to do whatever experiments he wanted, as long as they were for the good of Konoha. His team had left him behind a long time ago and he had nothing left to hold onto. Root members were fragile in the most unexpected of ways and as the months and eventual years passed with Orochimaru in their midst, they shifted and changed and became something more.

It was Orochimaru they went to when they had problems, when they needed help and it was his ideals (as twisted as they were) that they adopted. And in the end, something had to break.

They were to sabotage a mission run by Hatake Sakumo, one of the best jounin's of Konoha and spread malicious rumors about him when he failed it. It would break him and as close to war as they were, that wasn't something Konoha could get away with unscathed. It was a problem they had never encountered before. Loyalty to Danzo was supposed to be before all, but they had learned loyalty to Konoha's best from Orochimaru. They settled it like they did all problems they had.

They asked Orochimaru.

Distracted as he was by the experiments he was running (he'd succeeded with transplanting the Mokuton on a boy Kira called Tenzo) Orochimaru wasn't listening to what they were saying. He heard _Hatake_ and  _loyalty_ and _problem_ and _sabotage_ and in the end, all he mumbled about in response was, "Talk to the Hokage." 

It was a course of action they never would have taken on their own.

In the end, something had to break.

 

(And so came the last page.)

 

In the middle of the briefing for Hatake Sakumo's next mission in the Hokage's office, the room was invaded by three ANBU members wearing masks the Hokage didn't recognize. 

Instead of attacking, they took off their masks. What followed was an explanation of the mission given to them by Danzo-sama and Sarutobi found himself frozen in his seat as he was confronted by his old teammates actions. He'd suspected, but to think it was true... it pointed to a horrifying image. After the explanation was finished and Sarutobi had asked all the questions he immediately wanted to, he put out his pipe, leaned back on his chair and asked them, "Why tell me this now? I assume this is against Danzo's orders."

They looked at him as if they did not understand the question. The one in the middle, a girl that couldn't be older then fifteen, answered, "Because Orochimaru-sama told us to."

 

(Think of it as an epilogue.)

 

It ended kind of like this:

Orochimaru was summoned to the Hokage's office on his way home and when he arrived, it was to the presence of a grim faced Sarutobi Hiruzen and a Hatake Sakumo that somehow had something like relief and gratefulness in his eyes. After that, there were many meetings and interrogations and questions that he answered to the best of his ability while painting Danzo in the worst possible light he could, because he could be petty as well.

The fact that Sarutobi-sensei didn't stop him told him exactly how angry he was.

While Shimura Danzo was detained and later executed, Orochimaru was presented with a new office in the Hokage tower, bewildered and unable to understand what was happening. Root members were being questioned left and right and went from struggling to cooperating at an approving look from Orochimaru and Sarutobi just ended up more convinced that he'd failed his student and didn't know him at all.

Two weeks later, the door to Orochimaru's new office was blown wide open as a beaming Hatake bounced through the doorway, dragging behind him a tiny miniature with flyaway silver hair.

With another grin and a tug at a small resisting hand, Hatake Sakumo opened his mouth and demanded, with his eyes crinkled in delight, "Come to dinner with us. I need to thank you for preventing my mission to fail disastrously and Kakashi is a big fan of yours."

 

In the end, something had to break.

**Author's Note:**

> This is... yeah... let's just pretend it makes sense and leave it at that, okay?


End file.
